1. Technical Field
The present invention relates to an optical scanner; and more particularly, an optical scanner for fluorescence monitoring of an optical device, such as a microarray or biochip (spotted array or other biochip format), or other suitable optical device.
2. Description of Related Art
A common class of experiments, known as a multiplexed assay or multiplexed experiment, comprises mixing (or reacting) a labeled target analyte or sample (which may have known or unknown properties or sequences) with a set of “probe” or reference substances (which also may have known or unknown properties or sequences). Multiplexing allows many properties of the target analyte to be probed or evaluated simultaneously (i.e., in parallel). For example, in a gene expression assay, the “target” analyte, usually an unknown sequence of DNA, is labeled with a fluorescent molecule to form the labeled analyte.
In a known DNA/genomic sequencing assay, each probe consists of known DNA sequences of a predetermined length, which are attached to a labeled (or encoded) bead or to a known location on a substrate.
When the labeled target analyte is mixed with the probes, segments of the DNA sequence of the labeled target analyte will selectively bind to complementary segments of the DNA sequence of the known probe. The known probes are then spatially separated and examined for fluorescence. The beads that fluoresce indicate that the DNA sequence strands of the target analyte have attached or hybridized to the complementary DNA on that bead. The DNA sequences in the target analyte can then be determined by knowing the complementary DNA (or cDNA) sequence of each known probe to which the labeled target is attached. In addition the level of fluorescence is indicative of how many of the target molecules hybridized to the probe molecules for a given bead.
Generally, the probes are either spatially separated or otherwise labeled to identify the probe, and ultimately the “target” analyte. One approach separates the probes in a predetermined grid, where the probe's identity is linked to its position on the grid. One example of this is a “chip” format, where DNA is attached to a 2-D substrate, biochip or microarray, where oligomer DNA sequences are selectively attached (either by spotting or grown) onto small sections or spots on the surface of the substrate in a predetermined spatial order and location on a substrate (usually a planar substrate, such as a glass microscope slide).
However, in the prior art it is known that fluorescence signals vary strongly across the biochip or microarray, e.g. spotted array, due to:                Different degrees of hybridization; and        Different fluorescence efficiency.The reader is referred to FIG. 1A, which shows the basic problem in the art related to the variation of the fluorescence signals across a micromirror. Moreover, different arrays/tests may require different fluorescence markers; two is typical, but often more are used; and bulk-optic filters and filter wheels are often used to allow detection of different fluorescence spectra, but these devices are not flexible and readily scalable.        
Moreover, in the prior art it is also known that fluorescence signals vary strongly across a biochip or microarray (e.g. spotted array) due to different degrees of hybridization. See FIG. 1B, which sets forth another basic problem in the art related to the variation of the fluorescence signals across a micromirror. A wide dynamic range in the known detection system is required to measure all the expersion activity.
In view of this, there is a need in the art for an optical scanner to overcome the shortcomings of the known prior art scanners.